Higher oil recovery after waterflood in carbonate reservoirs is attributed to increasing water wettability of the rock that in turn relies on complicated surface chemistry. In addition, calcite mineral reacts with aqueous solutions and can alter substantially the composition of injected water by mineral dissolution. Carefully designed chemical and/or brine flood compositions in the laboratory may not remain intact while the injected solutions pass through the reactive reservoir rock. This is especially true for a low-salinity waterflood process, where some finely tuned brine compositions can improve flood performances, whereas others cannot. We present a 1D reactive transport numerical model that captures the changes in injected compositions during water flow through porous carbonate rock. We include highly coupled bulk aqueous and surface carbonate-reaction chemistry, detailed reaction and mass transfer kinetics, 2:1 calcium ion exchange, and axial dispersion. At typical calcite reaction rates, local equilibrium is established immediately upon injection. In SI, we validate the reactive transport model against analytic solutions for rock dissolution, ion exchange, and longitudinal dispersion, each considered separately. Accordingly, using an open-source algorithm (Charlton and Parkhurst in Comput Geosci 37(10):1653–1663, 2011. https://doi.org/10.1016/j.cageo.2011.02.005), we outline a design tool to specify chemical/brine flooding formulations that correct for composition alteration by the carbonate rock. Subsequent works compare proposed theory against experiments on core plugs of Indiana limestone and give examples of how injected salinity compositions deviate from those designed in the laboratory for water-wettability improvement.